Structural Chemogenomics Group

Laboratoire d'Innovation Therapeutique, UMR7200 CNRS/Universite de Strasbourg

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Software

Name Language Description
IChem 5.2.8 C++ A toolkit to detect, analyze and compare protein-ligand interactions encompassing most tools developed by our lab in the last 3 years

Marcou, G. and Rognan, D. (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints.J. Chem. Inf. Model., 47, 195-207
Desaphy, J., Azdimousa, K., and Rognan, D. (2012) Comparison and druggability prediction of protein-ligand binding pockets from pharmacophore-annotated shapes., J. Chem. Inf. Model., 52, 2287-2299
Desaphy, J., Ducrot, P., Raimbaud, E. and Rognan, D. (2013) Encoding protein-ligand interaction patterns in fingerprints and graphs. J. Chem. Inf. Model, 53, 623-637
Desaphy, J. and Rognan, D. (2014) scPDBFrag: a database of protein-ligand interaction patterns for bioisosteric replacements. J.Chem. Inf. Model., 54, 1908-1918
Gabel, J., Desaphy, J. and Rognan, D. (2014) Beware of machine learning-based scoring functions - On the danger of developing black boxes. J. Chem. Inf. Model, 54, 2807-2815
Da Silva, F., Desaphy, J., Bret, G. and Rognan, D. (2015) IChemPIC: A random forest classifier of biological and crystallographic protein-protein interfaces. J. Chem. Inf. Model, 55, 2005-2014
Slynko, I. Da Silva, F., Bret, G. and Rognan, D. (2016) Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015. J. Comput.-Aided Mol. Des., 30, 669-683

License key upon request to Dr. Didier Rognan (rognan[@]unistra.fr)
Shaper C++ Shape-based alignment of pharmacophore-annotated VolSite cavities
Avaiblable upon request to Dr. Didier Rognan (rognan[@]unistra.fr)
SiteAlign 4.0 C A simple and fuzzy method to align and compare druggable protein binding sites (Schalon et al., Proteins, 2008)
Licence file upon request to Dr. Didier Rognan (rognan[@]unistra.fr)
FuzCav Java A novel alignment-free high-throughput algorithm to compute pairwise similarities between protein_ligand binding sites ( Weill et al. , J Chem Info Model, 2010 )
FingerPrintLib C++ Computes molecular interaction fingerprints (Marcou et al. J Chem Info Model, 2007 )
pymolFP Python Interaction fingerprints viewer integrated in a pymol plugin
Fresno C++ Empirical scoring function (Rognan et al. J Med Chem, 1999 )

Datasets

File Description
PPIome dataset Druggable cavities/Ligands at and nearby protein-protein interfaces from the Protein Data Bank
Fragdock dataset 2376 ligand/protein structures aligned describing 64 different proteins.
Input/Output files for detecting PPIs and related cavities Input/Output files for detetecting PPIs and relasted cavities
PDBBind Test set PDBbind Test Set: 195 protein-ligand complexes (curated mol2 files).
Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014
Mod-PDBbind Set of decoy poses (0-5 Ang. rmsd to X-ray) for the 195 PDBbind test ligands
Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014
DUD-E docking poses Protein, ligand and docked poses for 10 DUD-E activity classes
Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014
Docking.tar.gz Docking dataset: 100 input files (protein, active site, ligand) from Kellenberger and al. Protein, 2004
Screening.zip Virtual screening datasets: Input files for receptor and ligand database (10 actives + 990 decoys) for both the tymidine kinase and the estrogen receptor alpha from Bissantz and al., J Med Chem, 2000

Miscellaneous tools

Name Language Description
bestGoldScorer Java Recover the best or all GOLD poses according yours requirements.
marvinEditButton PHP Marvin edit button extension is a mediawiki extension to draw compounds in Mediawiki.